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Full Structure Modeling of Three-Domains Monooxygenase CYP102A1 ВМ3 from Bacillus megaterium

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Moscow University Chemistry Bulletin Aims and scope

Abstract

The 3D full-atom model of the whole-size CYP102A1 from Bacillus megaterium (cytochrome P450 BM3) has been constructed using molecular modeling methods. The structure model was constructed using crystal structures of the separate FAD-binding domain (PDB ID: 4DQK) and the complex of FMN-binding and monooxygenase domains (PDB ID: 1BVY). Modeling procedure included analysis of the domains’ surfaces to find the orientation with maximum inter-subunit contacts. The overall configuration of the obtained complex was optimized using molecular dynamics. The final full-atom structure model shows rather tight interactions between FAD- and FMN-binding domains due to 10 inter-domain hydrogen bonds and hydrophobic interactions between three pairs of amino acid residues. This 3D model can be used for structure-function studies and rational design of the enzyme as well as for construction of hybrid supramolecular structures of biocatalysts with cytochrome P450 BM3.

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ACKNOWLEDGMENTS

This work was performed using the equipment of the shared research facilities of HPC computing resources at the Moscow State University [20].

Funding

This work was partially supported by the Russian Science Foundation (project no. 18-74-00146).

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Authors and Affiliations

  1. Dmitry Mendeleev University of Chemical Technology, Moscow, Russia

    A. V. Krivitskaya

  2. Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia

    A. A. Pometun, P. D. Parshin, M. G. Khrenova & V. I. Tishkov

  3. A.N. Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, Russia

    A. V. Krivitskaya, A. A. Pometun, M. G. Khrenova & V. I. Tishkov

  4. Innovations and High Technologies MSU Ltd., Moscow, Russia

    A. A. Pometun, P. D. Parshin & V. I. Tishkov

  5. Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    V. B. Urlacher

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  1. A. V. Krivitskaya
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  2. A. A. Pometun
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  6. V. I. Tishkov
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Correspondence to A. A. Pometun or V. I. Tishkov.

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Krivitskaya, A.V., Pometun, A.A., Parshin, P.D. et al. Full Structure Modeling of Three-Domains Monooxygenase CYP102A1 ВМ3 from Bacillus megaterium. Moscow Univ. Chem. Bull. 75, 162–166 (2020). https://doi.org/10.3103/S0027131420030074

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